Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2019 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 :
23 : #define cutOffNB 0.60 // buffer distance for neighbour-lists
24 : #define cutOffDist 0.50 // cut off distance for non-bonded pairwise forces
25 : #define cutOnDist 0.32 // cut off distance for non-bonded pairwise forces
26 : #define cutOffNB2 cutOffNB*cutOffNB // squared buffer distance for neighbour-lists
27 : #define cutOffDist2 cutOffDist*cutOffDist
28 : #define cutOnDist2 cutOnDist*cutOnDist
29 : #define invswitch 1.0/((cutOffDist2-cutOnDist2)*(cutOffDist2-cutOnDist2)*(cutOffDist2-cutOnDist2))
30 : #define cutOffDist4 cutOffDist2*cutOffDist2
31 : #define cutMixed cutOffDist2*cutOffDist2*cutOffDist2 -3.*cutOffDist2*cutOffDist2*cutOnDist2
32 :
33 : #include <string>
34 : #include <fstream>
35 : #include <iterator>
36 : #include <sstream>
37 :
38 : #include "MetainferenceBase.h"
39 : #include "core/ActionRegister.h"
40 : #include "tools/Pbc.h"
41 : #include "tools/PDB.h"
42 : #include "tools/Torsion.h"
43 :
44 : using namespace std;
45 :
46 : namespace PLMD {
47 : namespace isdb {
48 :
49 : //+PLUMEDOC ISDB_COLVAR CS2BACKBONE
50 : /*
51 : Calculates the backbone chemical shifts for a protein.
52 :
53 : The functional form is that of CamShift \cite Kohlhoff:2009us. The chemical shift
54 : of the selected nuclei can be saved as components. Alternatively one can calculate either
55 : the CAMSHIFT score (useful as a collective variable \cite Granata:2013dk or as a scoring
56 : function \cite Robustelli:2010dn) or a \ref METAINFERENCE score (using DOSCORE).
57 : For these two latter cases experimental chemical shifts must be provided.
58 :
59 : CS2BACKBONE calculation can be relatively heavy because it often uses a large number of atoms, it can
60 : be run in parallel using MPI and \ref Openmp.
61 :
62 : As a general rule, when using \ref CS2BACKBONE or other experimental restraints it may be better to
63 : increase the accuracy of the constraint algorithm due to the increased strain on the bonded structure.
64 : In the case of GROMACS it is safer to use lincs-iter=2 and lincs-order=6.
65 :
66 : In general the system for which chemical shifts are calculated must be completely included in
67 : ATOMS and a TEMPLATE pdb file for the same atoms should be provided as well in the folder DATADIR.
68 : The system is made automatically whole unless NOPBC is used, in particular if the system is made
69 : by multiple chains it is usually better to use NOPBC and make the molecule whole \ref WHOLEMOLECULES
70 : selecting an appropriate order of the atoms. The pdb file is needed to the generate a simple topology of the protein.
71 : For histidine residues in protonation states different from D the HIE/HSE HIP/HSP name should be used.
72 : GLH and ASH can be used for the alternative protonation of GLU and ASP. Non-standard amino acids and other
73 : molecules are not yet supported, but in principle they can be named UNK. If multiple chains are present
74 : the chain identifier must be in the standard PDB format, together with the TER keyword at the end of each chain.
75 : Termini groups like ACE or NME should be removed from the TEMPLATE pdb because they are not recognized by
76 : CS2BACKBONE.
77 :
78 : In addition to a pdb file one needs to provide a list of chemical shifts to be calculated using one
79 : file per nucleus type (CAshifts.dat, CBshifts.dat, Cshifts.dat, Hshifts.dat, HAshifts.dat, Nshifts.dat),
80 : add only the files for the nuclei you need, but each file should include all protein residues.
81 : A chemical shift for a nucleus is calculated if a value greater than 0 is provided.
82 : For practical purposes the value can correspond to the experimental value.
83 : Residues numbers should match that used in the pdb file, but must be positive, so double check the pdb.
84 : The first and last residue of each chain should be preceded by a # character.
85 :
86 : \verbatim
87 : CAshifts.dat:
88 : #1 0.0
89 : 2 55.5
90 : 3 58.4
91 : .
92 : .
93 : #last 0.0
94 : #first of second chain
95 : .
96 : #last of second chain
97 : \endverbatim
98 :
99 : The default behavior is to store the values for the active nuclei in components (ca-#, cb-#,
100 : co-#, ha-#, hn-#, nh-# and expca-#, expcb-#, expco-#, expha-#, exphn-#, exp-nh#) with NOEXP it is possible
101 : to only store the back-calculated values, where # includes a chain and residue number.
102 :
103 : One additional file is always needed in the folder DATADIR: camshift.db. This file includes all the parameters needed to
104 : calculate the chemical shifts and can be found in regtest/isdb/rt-cs2backbone/data/ .
105 :
106 : Additional material and examples can be also found in the tutorial \ref belfast-9 as well as in the cs2backbone regtests
107 : in the isdb folder.
108 :
109 : \par Examples
110 :
111 : In this first example the chemical shifts are used to calculate a collective variable to be used
112 : in NMR driven Metadynamics \cite Granata:2013dk :
113 :
114 : \plumedfile
115 : whole: GROUP ATOMS=2612-2514:-1,961-1:-1,2466-962:-1,2513-2467:-1
116 : WHOLEMOLECULES ENTITY0=whole
117 : cs: CS2BACKBONE ATOMS=1-2612 DATADIR=data/ TEMPLATE=template.pdb CAMSHIFT NOPBC
118 : metad: METAD ARG=cs HEIGHT=0.5 SIGMA=0.1 PACE=200 BIASFACTOR=10
119 : PRINT ARG=cs,metad.bias FILE=COLVAR STRIDE=100
120 : \endplumedfile
121 :
122 : In this second example the chemical shifts are used as replica-averaged restrained as in \cite Camilloni:2012je \cite Camilloni:2013hs.
123 :
124 : \plumedfile
125 : cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/
126 : encs: ENSEMBLE ARG=(cs\.hn-.*),(cs\.nh-.*)
127 : stcs: STATS ARG=encs.* SQDEVSUM PARARG=(cs\.exphn-.*),(cs\.expnh-.*)
128 : RESTRAINT ARG=stcs.sqdevsum AT=0 KAPPA=0 SLOPE=24
129 :
130 : PRINT ARG=(cs\.hn-.*),(cs\.nh-.*) FILE=RESTRAINT STRIDE=100
131 :
132 : \endplumedfile
133 :
134 : This third example show how to use chemical shifts to calculate a \ref METAINFERENCE score .
135 :
136 : \plumedfile
137 : cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/ SIGMA_MEAN0=1.0 DOSCORE
138 : csbias: BIASVALUE ARG=cs.score
139 :
140 : PRINT ARG=(cs\.hn-.*),(cs\.nh-.*) FILE=CS.dat STRIDE=1000
141 : PRINT ARG=cs.score FILE=BIAS STRIDE=100
142 : \endplumedfile
143 :
144 : */
145 : //+ENDPLUMEDOC
146 :
147 : class CS2BackboneDB {
148 : enum { STD, GLY, PRO};
149 : enum { HA_ATOM, H_ATOM, N_ATOM, CA_ATOM, CB_ATOM, C_ATOM };
150 : static const unsigned aa_kind = 3;
151 : static const unsigned atm_kind = 6;
152 : static const unsigned numXtraDists = 27;
153 :
154 : // ALA, ARG, ASN, ASP, CYS, GLU, GLN, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL
155 : double c_aa[aa_kind][atm_kind][20];
156 : double c_aa_prev[aa_kind][atm_kind][20];
157 : double c_aa_succ[aa_kind][atm_kind][20];
158 : double co_bb[aa_kind][atm_kind][16];
159 : double co_sc_[aa_kind][atm_kind][20][20];
160 : double co_xd[aa_kind][atm_kind][numXtraDists];
161 : double co_sphere[aa_kind][atm_kind][2][8];
162 : // for ring current effects
163 : // Phe, Tyr, Trp_1, Trp_2, His
164 : double co_ring[aa_kind][atm_kind][5];
165 : // for dihedral angles
166 : // co * (a * cos(3 * omega + c) + b * cos(omega + d))
167 : double co_da[aa_kind][atm_kind][3];
168 : double pars_da[aa_kind][atm_kind][3][5];
169 :
170 : public:
171 :
172 10926 : inline unsigned kind(const string &s) {
173 10926 : if(s=="GLY") return GLY;
174 9324 : else if(s=="PRO") return PRO;
175 9108 : return STD;
176 : }
177 :
178 10926 : inline unsigned atom_kind(const string &s) {
179 10926 : if(s=="HA")return HA_ATOM;
180 10872 : else if(s=="H") return H_ATOM;
181 8010 : else if(s=="N") return N_ATOM;
182 5148 : else if(s=="CA")return CA_ATOM;
183 2160 : else if(s=="CB")return CB_ATOM;
184 54 : else if(s=="C") return C_ATOM;
185 0 : return -1;
186 : }
187 :
188 : unsigned get_numXtraDists() {return numXtraDists;}
189 :
190 : //PARAMETERS
191 : inline double * CONSTAACURR(const unsigned a_kind, const unsigned at_kind) {return c_aa[a_kind][at_kind];}
192 : inline double * CONSTAANEXT(const unsigned a_kind, const unsigned at_kind) {return c_aa_succ[a_kind][at_kind];}
193 : inline double * CONSTAAPREV(const unsigned a_kind, const unsigned at_kind) {return c_aa_prev[a_kind][at_kind];}
194 : inline double * CONST_BB2(const unsigned a_kind, const unsigned at_kind) {return co_bb[a_kind][at_kind];}
195 : inline double * CONST_SC2(const unsigned a_kind, const unsigned at_kind, unsigned res_type) { return co_sc_[a_kind][at_kind][res_type];}
196 : inline double * CONST_XD(const unsigned a_kind, const unsigned at_kind) { return co_xd[a_kind][at_kind];}
197 : inline double * CO_SPHERE(const unsigned a_kind, const unsigned at_kind, unsigned exp_type) { return co_sphere[a_kind][at_kind][exp_type];}
198 : inline double * CO_RING(const unsigned a_kind, const unsigned at_kind) { return co_ring[a_kind][at_kind];}
199 : inline double * CO_DA(const unsigned a_kind, const unsigned at_kind) { return co_da[a_kind][at_kind];}
200 : inline double * PARS_DA(const unsigned a_kind, const unsigned at_kind, const unsigned ang_kind) { return pars_da[a_kind][at_kind][ang_kind];}
201 :
202 18 : void parse(const string &file, const double dscale) {
203 18 : ifstream in;
204 18 : in.open(file.c_str());
205 18 : if(!in) plumed_merror("Unable to open DB file: " + file);
206 :
207 : unsigned c_kind = 0;
208 : unsigned c_atom = 0;
209 : unsigned nline = 0;
210 :
211 324 : for(unsigned i=0; i<3; i++) for(unsigned j=0; j<6; j++) {
212 6480 : for(unsigned k=0; k<20; k++) {
213 6480 : c_aa[i][j][k]=0.;
214 6480 : c_aa_prev[i][j][k]=0.;
215 6480 : c_aa_succ[i][j][k]=0.;
216 6480 : for(unsigned m=0; m<20; m++) co_sc_[i][j][k][m]=0.;
217 : }
218 5184 : for(unsigned k=0; k<16; k++) {co_bb[i][j][k]=0.; }
219 2592 : for(unsigned k=0; k<8; k++) { co_sphere[i][j][0][k]=0.; co_sphere[i][j][1][k]=0.; }
220 972 : for(unsigned k=0; k<3; k++) {
221 972 : co_da[i][j][k]=0.;
222 972 : for(unsigned l=0; l<5; l++) pars_da[i][j][k][l]=0.;
223 : }
224 1620 : for(unsigned k=0; k<5; k++) co_ring[i][j][k]=0.;
225 8748 : for(unsigned k=0; k<numXtraDists; k++) co_xd[i][j][k]=0.;
226 : }
227 :
228 37710 : while(!in.eof()) {
229 : string line;
230 37692 : getline(in,line);
231 : ++nline;
232 37692 : if(line.compare(0,1,"#")==0) continue;
233 0 : vector<string> tok;
234 0 : vector<string> tmp;
235 40860 : tok = split(line,' ');
236 523656 : for(unsigned q=0; q<tok.size(); q++)
237 241398 : if(tok[q].size()) tmp.push_back(tok[q]);
238 20430 : tok = tmp;
239 40860 : if(tok.size()==0) continue;
240 20412 : if(tok[0]=="PAR") {
241 324 : c_kind = kind(tok[2]);
242 324 : c_atom = atom_kind(tok[1]);
243 : continue;
244 : }
245 20088 : else if(tok[0]=="WEIGHT") {
246 : continue;
247 : }
248 19764 : else if(tok[0]=="FLATBTM") {
249 : continue;
250 : }
251 19440 : else if (tok[0] == "SCALEHARM") {
252 : continue;
253 : }
254 19116 : else if (tok[0] == "TANHAMPLI") {
255 : continue;
256 : }
257 18792 : else if (tok[0] == "ENDHARMON") {
258 : continue;
259 : }
260 18468 : else if (tok[0] == "MAXRCDEVI") {
261 : continue;
262 : }
263 18144 : else if (tok[0] == "RANDCOIL") {
264 : continue;
265 : }
266 17820 : else if (tok[0] == "CONST") {
267 : continue;
268 : }
269 17496 : else if (tok[0] == "CONSTAA") {
270 324 : assign(c_aa[c_kind][c_atom],tok,1);
271 : continue;
272 : }
273 17172 : else if (tok[0] == "CONSTAA-1") {
274 324 : assign(c_aa_prev[c_kind][c_atom],tok,1);
275 : continue;
276 : }
277 16848 : else if (tok[0] == "CONSTAA+1") {
278 324 : assign(c_aa_succ[c_kind][c_atom],tok,1);
279 : continue;
280 : }
281 16524 : else if (tok[0] == "COBB1") {
282 : continue;
283 : }
284 16200 : else if (tok[0] == "COBB2") {
285 : //angstrom to nm
286 324 : assign(co_bb[c_kind][c_atom],tok,dscale);
287 : continue;
288 : }
289 15876 : else if (tok[0] == "SPHERE1") {
290 : // angstrom^-3 to nm^-3
291 324 : assign(co_sphere[c_kind][c_atom][0],tok,1./(dscale*dscale*dscale));
292 : continue;
293 : }
294 15552 : else if (tok[0] == "SPHERE2") {
295 : //angstrom to nm
296 324 : assign(co_sphere[c_kind][c_atom][1],tok,dscale);
297 : continue;
298 : }
299 15228 : else if (tok[0] == "DIHEDRALS") {
300 324 : assign(co_da[c_kind][c_atom],tok,1);
301 : continue;
302 : }
303 14904 : else if (tok[0] == "RINGS") {
304 : // angstrom^-3 to nm^-3
305 324 : assign(co_ring[c_kind][c_atom],tok,1./(dscale*dscale*dscale));
306 3888 : for(unsigned i=1; i<tok.size(); i++)
307 1620 : co_ring[c_kind][c_atom][i-1] *= 1000;
308 : continue;
309 : }
310 14580 : else if (tok[0] == "HBONDS") {
311 : continue;
312 : }
313 14256 : else if (tok[0] == "XTRADISTS") {
314 : //angstrom to nm
315 324 : assign(co_xd[c_kind][c_atom],tok,dscale);
316 : continue;
317 : }
318 13932 : else if(tok[0]=="DIHEDPHI") {
319 324 : assign(pars_da[c_kind][c_atom][0],tok,1);
320 : continue;
321 : }
322 13608 : else if(tok[0]=="DIHEDPSI") {
323 324 : assign(pars_da[c_kind][c_atom][1],tok,1);
324 : continue;
325 : }
326 13284 : else if(tok[0]=="DIHEDCHI1") {
327 324 : assign(pars_da[c_kind][c_atom][2],tok,1);
328 : continue;
329 : }
330 :
331 : bool ok = false;
332 : string scIdent1 [] = {"COSCALA1", "COSCARG1", "COSCASN1", "COSCASP1", "COSCCYS1", "COSCGLN1", "COSCGLU1",
333 : "COSCGLY1", "COSCHIS1", "COSCILE1", "COSCLEU1", "COSCLYS1", "COSCMET1", "COSCPHE1",
334 : "COSCPRO1", "COSCSER1", "COSCTHR1", "COSCTRP1", "COSCTYR1", "COSCVAL1"
335 12960 : };
336 :
337 204120 : for(unsigned scC = 0; scC < 20; scC++) {
338 395280 : if(tok[0]==scIdent1[scC]) {
339 : ok = true;
340 : break;
341 : }
342 : }
343 285120 : if(ok) continue;
344 :
345 : string scIdent2 [] = {"COSCALA2", "COSCARG2", "COSCASN2", "COSCASP2", "COSCCYS2", "COSCGLN2", "COSCGLU2",
346 : "COSCGLY2", "COSCHIS2", "COSCILE2", "COSCLEU2", "COSCLYS2", "COSCMET2", "COSCPHE2",
347 : "COSCPRO2", "COSCSER2", "COSCTHR2", "COSCTRP2", "COSCTYR2", "COSCVAL2"
348 6480 : };
349 :
350 68040 : for(unsigned scC = 0; scC < 20; scC++) {
351 136080 : if(tok[0]==scIdent2[scC]) {
352 : //angstrom to nm
353 6480 : assign(co_sc_[c_kind][c_atom][scC],tok,dscale);
354 6480 : ok = true; break;
355 : }
356 : }
357 142560 : if(ok) continue;
358 :
359 0 : if(tok.size()) {
360 0 : string str_err = "DB WARNING: unrecognized token: " + tok[0];
361 0 : plumed_merror(str_err);
362 : }
363 : }
364 18 : in.close();
365 18 : }
366 :
367 : private:
368 :
369 20430 : vector<string> &split(const string &s, char delim, vector<string> &elems) {
370 20430 : stringstream ss(s);
371 : string item;
372 523656 : while (getline(ss, item, delim)) {
373 241398 : elems.push_back(item);
374 : }
375 20430 : return elems;
376 : }
377 :
378 20430 : vector<string> split(const string &s, char delim) {
379 : vector<string> elems;
380 20430 : split(s, delim, elems);
381 20430 : return elems;
382 : }
383 :
384 10368 : void assign(double * f, const vector<string> & v, const double scale) {
385 245592 : for(unsigned i=1; i<v.size(); i++) {
386 224856 : f[i-1] = scale*(atof(v[i].c_str()));
387 112428 : if(fabs(f[i-1])<0.000001) f[i-1]=0.;
388 : }
389 10368 : }
390 : };
391 :
392 54 : class CS2Backbone : public MetainferenceBase {
393 145080 : struct ChemicalShift {
394 : double exp_cs; // a reference chemical shifts
395 : Value *comp; // a pointer to the component
396 : unsigned res_kind; // residue type (STD/GLY/PRO)
397 : unsigned atm_kind; // nuclues (HA/CA/CB/CO/NH/HN)
398 : unsigned res_type_prev; // previuos residue (ALA/VAL/..)
399 : unsigned res_type_curr; // current residue (ALA/VAL/..)
400 : unsigned res_type_next; // next residue (ALA/VAL/..)
401 : string res_name; // residue name
402 : string nucleus; // chemical shift
403 : bool has_chi1; // does we have a chi1
404 : unsigned csatoms; // fixed number of atoms used
405 : unsigned totcsatoms; // number of atoms used
406 : unsigned res_num; // residue number
407 : unsigned chain; // chain number
408 : unsigned ipos; // index of the atom for which we are calculating the chemical shifts
409 : vector<unsigned> bb; // atoms for the previous, current and next backbone
410 : vector<unsigned> side_chain;// atoms for the current sidechain
411 : vector<int> xd1; // additional couple of atoms
412 : vector<int> xd2; // additional couple of atoms
413 : vector<unsigned> box_nb; // non-bonded atoms
414 :
415 10602 : ChemicalShift():
416 : exp_cs(0.),
417 : comp(NULL),
418 : res_kind(0),
419 : atm_kind(0),
420 : res_type_prev(0),
421 : res_type_curr(0),
422 : res_type_next(0),
423 : res_name(""),
424 : nucleus(""),
425 : has_chi1(true),
426 : csatoms(0),
427 : totcsatoms(0),
428 : res_num(0),
429 : chain(0),
430 10602 : ipos(0)
431 : {
432 10602 : xd1.reserve(26);
433 10602 : xd2.reserve(26);
434 10602 : box_nb.reserve(150);
435 10602 : }
436 : };
437 :
438 : struct RingInfo {
439 : enum {R_PHE, R_TYR, R_TRP1, R_TRP2, R_HIS};
440 : unsigned rtype; // one out of five different types
441 : unsigned atom[6]; // up to six member per ring
442 : unsigned numAtoms; // number of ring members (5 or 6)
443 : Vector position; // center of ring coordinates
444 : Vector normVect; // ring plane normal vector
445 : Vector g[6]; // vector of the vectors used for normVect
446 : double lengthN2; // square of length of normVect
447 : double lengthNV; // length of normVect
448 360 : RingInfo():
449 : rtype(0),
450 : numAtoms(0),
451 : lengthN2(NAN),
452 360 : lengthNV(NAN)
453 : {
454 360 : for(unsigned i=0; i<6; i++) atom[i]=0;
455 360 : }
456 : };
457 :
458 : enum aa_t {ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, UNK};
459 : enum sequence_t {Np, CAp, HAp, Cp, Op, Nc, Hc, CAc, HAc, Cc, Oc, Nn, Hn, CAn, HAn, Cn, CBc, CGc};
460 :
461 : CS2BackboneDB db;
462 : vector<ChemicalShift> chemicalshifts;
463 :
464 : vector<RingInfo> ringInfo;
465 : vector<unsigned> type;
466 : vector<unsigned> res_num;
467 : unsigned max_cs_atoms;
468 : unsigned box_nupdate;
469 : unsigned box_count;
470 : bool camshift;
471 : bool pbc;
472 : bool serial;
473 :
474 : void init_cs(const string &file, const string &k, const PDB &pdb);
475 : void update_neighb();
476 : void compute_ring_parameters();
477 : void init_types(const PDB &pdb);
478 : void init_rings(const PDB &pdb);
479 : aa_t frag2enum(const string &aa);
480 : vector<string> side_chain_atoms(const string &s);
481 : bool isSP2(const string & resType, const string & atomName);
482 : bool is_chi1_cx(const string & frg, const string & atm);
483 : void xdist_name_map(string & name);
484 :
485 : public:
486 :
487 : explicit CS2Backbone(const ActionOptions&);
488 : static void registerKeywords( Keywords& keys );
489 : void calculate() override;
490 : void update() override;
491 : };
492 :
493 7868 : PLUMED_REGISTER_ACTION(CS2Backbone,"CS2BACKBONE")
494 :
495 19 : void CS2Backbone::registerKeywords( Keywords& keys ) {
496 19 : componentsAreNotOptional(keys);
497 19 : MetainferenceBase::registerKeywords( keys );
498 57 : keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
499 57 : keys.addFlag("SERIAL",false,"Perform the calculation in serial - for debug purpose");
500 76 : keys.add("atoms","ATOMS","The atoms to be included in the calculation, e.g. the whole protein.");
501 95 : keys.add("compulsory","DATADIR","data/","The folder with the experimental chemical shifts.");
502 95 : keys.add("compulsory","TEMPLATE","template.pdb","A PDB file of the protein system to initialize ALMOST.");
503 95 : keys.add("compulsory","NEIGH_FREQ","20","Period in step for neighbor list update.");
504 57 : keys.addFlag("CAMSHIFT",false,"Set to TRUE if you to calculate a single CamShift score.");
505 57 : keys.addFlag("NOEXP",false,"Set to TRUE if you don't want to have fixed components with the experimental values.");
506 76 : keys.addOutputComponent("ha","default","the calculated Ha hydrogen chemical shifts");
507 76 : keys.addOutputComponent("hn","default","the calculated H hydrogen chemical shifts");
508 76 : keys.addOutputComponent("nh","default","the calculated N nitrogen chemical shifts");
509 76 : keys.addOutputComponent("ca","default","the calculated Ca carbon chemical shifts");
510 76 : keys.addOutputComponent("cb","default","the calculated Cb carbon chemical shifts");
511 76 : keys.addOutputComponent("co","default","the calculated C' carbon chemical shifts");
512 76 : keys.addOutputComponent("expha","default","the experimental Ha hydrogen chemical shifts");
513 76 : keys.addOutputComponent("exphn","default","the experimental H hydrogen chemical shifts");
514 76 : keys.addOutputComponent("expnh","default","the experimental N nitrogen chemical shifts");
515 76 : keys.addOutputComponent("expca","default","the experimental Ca carbon chemical shifts");
516 76 : keys.addOutputComponent("expcb","default","the experimental Cb carbon chemical shifts");
517 76 : keys.addOutputComponent("expco","default","the experimental C' carbon chemical shifts");
518 19 : }
519 :
520 18 : CS2Backbone::CS2Backbone(const ActionOptions&ao):
521 : PLUMED_METAINF_INIT(ao),
522 : max_cs_atoms(0),
523 : camshift(false),
524 : pbc(true),
525 36 : serial(false)
526 : {
527 : vector<AtomNumber> used_atoms;
528 36 : parseAtomList("ATOMS",used_atoms);
529 :
530 36 : parseFlag("CAMSHIFT",camshift);
531 23 : if(camshift&&getDoScore()) plumed_merror("It is not possible to use CAMSHIFT and DOSCORE at the same time");
532 :
533 18 : bool nopbc=!pbc;
534 36 : parseFlag("NOPBC",nopbc);
535 18 : pbc=!nopbc;
536 :
537 36 : parseFlag("SERIAL",serial);
538 :
539 18 : bool noexp=false;
540 36 : parseFlag("NOEXP",noexp);
541 :
542 : string stringa_data;
543 36 : parse("DATADIR",stringa_data);
544 :
545 : string stringa_template;
546 36 : parse("TEMPLATE",stringa_template);
547 :
548 18 : box_count=0;
549 18 : box_nupdate=20;
550 36 : parse("NEIGH_FREQ", box_nupdate);
551 :
552 36 : string stringadb = stringa_data + string("/camshift.db");
553 54 : string stringapdb = stringa_data + string("/") + stringa_template;
554 :
555 : /* Lenght conversion (parameters are tuned for angstrom) */
556 : double scale=1.;
557 36 : if(!plumed.getAtoms().usingNaturalUnits()) {
558 18 : scale = 10.*atoms.getUnits().getLength();
559 : }
560 :
561 18 : log.printf(" Initialization of the predictor ...\n");
562 18 : db.parse(stringadb,scale);
563 :
564 36 : PDB pdb;
565 36 : if( !pdb.read(stringapdb,plumed.getAtoms().usingNaturalUnits(),1./scale) ) plumed_merror("missing input file " + stringapdb);
566 :
567 : // first of all we build the list of chemical shifts we want to predict
568 18 : log.printf(" Reading experimental data ...\n"); log.flush();
569 54 : stringadb = stringa_data + string("/CAshifts.dat");
570 18 : log.printf(" Initializing CA shifts %s\n", stringadb.c_str());
571 36 : init_cs(stringadb, "CA", pdb);
572 54 : stringadb = stringa_data + string("/CBshifts.dat");
573 18 : log.printf(" Initializing CB shifts %s\n", stringadb.c_str());
574 36 : init_cs(stringadb, "CB", pdb);
575 54 : stringadb = stringa_data + string("/Cshifts.dat");
576 18 : log.printf(" Initializing C' shifts %s\n", stringadb.c_str());
577 36 : init_cs(stringadb, "C", pdb);
578 54 : stringadb = stringa_data + string("/HAshifts.dat");
579 18 : log.printf(" Initializing HA shifts %s\n", stringadb.c_str());
580 36 : init_cs(stringadb, "HA", pdb);
581 54 : stringadb = stringa_data + string("/Hshifts.dat");
582 18 : log.printf(" Initializing H shifts %s\n", stringadb.c_str());
583 36 : init_cs(stringadb, "H", pdb);
584 54 : stringadb = stringa_data + string("/Nshifts.dat");
585 18 : log.printf(" Initializing N shifts %s\n", stringadb.c_str());
586 36 : init_cs(stringadb, "N", pdb);
587 :
588 18 : if(chemicalshifts.size()==0) plumed_merror("There are no chemical shifts to calculate, there must be at least a not empty file (CA|CB|C|HA|H|N|shifts.dat)");
589 :
590 18 : init_types(pdb);
591 18 : init_rings(pdb);
592 :
593 18 : log<<" Bibliography "
594 72 : <<plumed.cite("Kohlhoff K, Robustelli P, Cavalli A, Salvatella A, Vendruscolo M, J. Am. Chem. Soc. 131, 13894 (2009)");
595 28 : if(camshift) log<<plumed.cite("Granata D, Camilloni C, Vendruscolo M, Laio A, Proc. Natl. Acad. Sci. USA 110, 6817 (2013)");
596 39 : else log<<plumed.cite("Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)");
597 54 : log<<plumed.cite("Bonomi M, Camilloni C, Bioinformatics, 33, 3999 (2017)");
598 18 : log<<"\n";
599 :
600 18 : if(camshift) {
601 5 : noexp = true;
602 5 : addValueWithDerivatives();
603 5 : setNotPeriodic();
604 : } else {
605 15327 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
606 7657 : std::string num; Tools::convert(chemicalshifts[cs].res_num,num);
607 7657 : std::string chain_num; Tools::convert(chemicalshifts[cs].chain,chain_num);
608 7657 : if(getDoScore()) {
609 11780 : addComponent(chemicalshifts[cs].nucleus+chain_num+"-"+num);
610 11780 : componentIsNotPeriodic(chemicalshifts[cs].nucleus+chain_num+"-"+num);
611 11780 : chemicalshifts[cs].comp = getPntrToComponent(chemicalshifts[cs].nucleus+chain_num+"-"+num);
612 2356 : setParameter(chemicalshifts[cs].exp_cs);
613 : } else {
614 26505 : addComponentWithDerivatives(chemicalshifts[cs].nucleus+chain_num+"-"+num);
615 26505 : componentIsNotPeriodic(chemicalshifts[cs].nucleus+chain_num+"-"+num);
616 26505 : chemicalshifts[cs].comp = getPntrToComponent(chemicalshifts[cs].nucleus+chain_num+"-"+num);
617 : }
618 : }
619 13 : if(getDoScore()) Initialise(chemicalshifts.size());
620 : }
621 :
622 18 : if(!noexp) {
623 15327 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
624 7657 : std::string num; Tools::convert(chemicalshifts[cs].res_num,num);
625 7657 : std::string chain_num; Tools::convert(chemicalshifts[cs].chain,chain_num);
626 45942 : addComponent("exp"+chemicalshifts[cs].nucleus+chain_num+"-"+num);
627 45942 : componentIsNotPeriodic("exp"+chemicalshifts[cs].nucleus+chain_num+"-"+num);
628 45942 : Value* comp=getPntrToComponent("exp"+chemicalshifts[cs].nucleus+chain_num+"-"+num);
629 7657 : comp->set(chemicalshifts[cs].exp_cs);
630 : }
631 : }
632 :
633 18 : requestAtoms(used_atoms, false);
634 18 : setDerivatives();
635 18 : checkRead();
636 18 : }
637 :
638 108 : void CS2Backbone::init_cs(const string &file, const string &nucl, const PDB &pdb) {
639 : // number of chains
640 : vector<string> chains;
641 108 : pdb.getChainNames( chains );
642 : unsigned ichain=0;
643 :
644 216 : ifstream in;
645 108 : in.open(file.c_str());
646 108 : if(!in) return;
647 108 : istream_iterator<string> iter(in), end;
648 : unsigned begin=0;
649 :
650 19116 : while(iter!=end) {
651 19008 : string tok = *iter;
652 : ++iter;
653 19008 : if(tok[0]=='#') {
654 : ++iter;
655 432 : if(begin==1) {
656 : begin=0;
657 216 : ichain++;
658 : } else begin=1;
659 : continue;
660 : }
661 : int ro = atoi(tok.c_str());
662 18576 : if(ro<0) plumed_merror("Residue numbers should be positive\n");
663 18576 : unsigned resnum = static_cast<unsigned> (ro);
664 : tok = *iter;
665 : ++iter;
666 : double cs = atof(tok.c_str());
667 18576 : if(cs==0) continue;
668 :
669 : unsigned fres, lres;
670 : string errmsg;
671 22140 : pdb.getResidueRange(chains[ichain], fres, lres, errmsg);
672 11070 : if(resnum==fres||resnum==lres) plumed_merror("First and Last residue of each chain should be annotated as # in " + file + " Remember that residue numbers should match");
673 :
674 : // check in the PDB for the chain/residue/atom and enable the chemical shift
675 11070 : string RES = pdb.getResidueName(resnum, chains[ichain]);
676 98766 : if(RES=="HIE"||RES=="HIP"||RES=="HIS"||RES=="HSP"||RES=="HSE"||RES=="CYS"||RES=="GLH"||RES=="ASH"||RES=="UNK") continue;
677 10944 : if(RES=="GLN"&&nucl=="CB") continue;
678 11322 : if(RES=="ILE"&&nucl=="CB") continue;
679 10998 : if(RES=="PRO"&&nucl=="N") continue;
680 10998 : if(RES=="PRO"&&nucl=="H") continue;
681 10998 : if(RES=="PRO"&&nucl=="CB") continue;
682 12240 : if(RES=="GLY"&&nucl=="HA") continue;
683 12240 : if(RES=="GLY"&&nucl=="CB") continue;
684 :
685 21204 : ChemicalShift tmp_cs;
686 :
687 10602 : tmp_cs.exp_cs = cs;
688 10602 : if(nucl=="CA") tmp_cs.nucleus = "ca-";
689 7668 : else if(nucl=="CB") tmp_cs.nucleus = "cb-";
690 5616 : else if(nucl=="C") tmp_cs.nucleus = "co-";
691 5616 : else if(nucl=="HA") tmp_cs.nucleus = "ha-";
692 5616 : else if(nucl=="H") tmp_cs.nucleus = "hn-";
693 2808 : else if(nucl=="N") tmp_cs.nucleus = "nh-";
694 10602 : tmp_cs.chain = ichain;
695 10602 : tmp_cs.res_num = resnum;
696 10602 : tmp_cs.res_type_curr = frag2enum(RES);
697 21204 : tmp_cs.res_type_prev = frag2enum(pdb.getResidueName(resnum-1, chains[ichain]));
698 21204 : tmp_cs.res_type_next = frag2enum(pdb.getResidueName(resnum+1, chains[ichain]));
699 : tmp_cs.res_name = RES;
700 10602 : tmp_cs.res_kind = db.kind(RES);
701 10602 : tmp_cs.atm_kind = db.atom_kind(nucl);
702 20556 : if(RES!="ALA"&&RES!="GLY") {tmp_cs.bb.resize(18); tmp_cs.has_chi1=true;}
703 2142 : else {tmp_cs.bb.resize(16); tmp_cs.has_chi1=false;}
704 :
705 10602 : vector<AtomNumber> res_atoms = pdb.getAtomsInResidue(resnum, chains[ichain]);
706 : // find the position of the nucleus and of the other backbone atoms as well as for phi/psi/chi
707 335934 : for(unsigned a=0; a<res_atoms.size(); a++) {
708 162666 : string AN = pdb.getAtomName(res_atoms[a]);
709 162666 : if(nucl=="HA"&&(AN=="HA"||AN=="HA1"||AN=="HA3")) tmp_cs.ipos = res_atoms[a].index();
710 247338 : else if(nucl=="H"&&(AN=="H"||AN=="HN")) tmp_cs.ipos = res_atoms[a].index();
711 205056 : else if(nucl=="N"&&AN=="N") tmp_cs.ipos = res_atoms[a].index();
712 203796 : else if(nucl=="CA"&&AN=="CA") tmp_cs.ipos = res_atoms[a].index();
713 190296 : else if(nucl=="CB"&&AN=="CB") tmp_cs.ipos = res_atoms[a].index();
714 152064 : else if(nucl=="C"&&AN=="C" ) tmp_cs.ipos = res_atoms[a].index();
715 : }
716 :
717 10602 : vector<AtomNumber> prev_res_atoms = pdb.getAtomsInResidue(resnum-1, chains[ichain]);
718 : // find the position of the previous residues backbone atoms
719 336996 : for(unsigned a=0; a<prev_res_atoms.size(); a++) {
720 157896 : string AN = pdb.getAtomName(prev_res_atoms[a]);
721 168498 : if(AN=="N") { tmp_cs.bb[Np] = prev_res_atoms[a].index(); }
722 157896 : else if(AN=="CA") { tmp_cs.bb[CAp] = prev_res_atoms[a].index(); }
723 401292 : else if(AN=="HA"||AN=="HA1"||AN=="HA3") { tmp_cs.bb[HAp] = prev_res_atoms[a].index(); }
724 136692 : else if(AN=="C" ) { tmp_cs.bb[Cp] = prev_res_atoms[a].index(); }
725 126090 : else if(AN=="O" ) { tmp_cs.bb[Op] = prev_res_atoms[a].index(); }
726 : }
727 :
728 335934 : for(unsigned a=0; a<res_atoms.size(); a++) {
729 162666 : string AN = pdb.getAtomName(res_atoms[a]);
730 173268 : if(AN=="N") { tmp_cs.bb[Nc] = res_atoms[a].index(); }
731 448884 : else if(AN=="H" ||AN=="HN"||(AN=="CD"&&RES=="PRO")) { tmp_cs.bb[Hc] = res_atoms[a].index(); }
732 152064 : else if(AN=="CA") { tmp_cs.bb[CAc] = res_atoms[a].index(); }
733 383472 : else if(AN=="HA"||AN=="HA1"||AN=="HA3") { tmp_cs.bb[HAc] = res_atoms[a].index(); }
734 130860 : else if(AN=="C" ) { tmp_cs.bb[Cc] = res_atoms[a].index(); }
735 120258 : else if(AN=="O" ) { tmp_cs.bb[Oc] = res_atoms[a].index(); }
736 :
737 318852 : if(RES!="ALA"&&RES!="GLY") {
738 154188 : if(AN=="CB") tmp_cs.bb[CBc] = res_atoms[a].index();
739 154188 : if(is_chi1_cx(RES,AN)) tmp_cs.bb[CGc] = res_atoms[a].index();
740 : }
741 : }
742 :
743 10602 : vector<AtomNumber> next_res_atoms = pdb.getAtomsInResidue(resnum+1, chains[ichain]);
744 10602 : string NRES = pdb.getResidueName(resnum+1, chains[ichain]);
745 : // find the position of the previous residues backbone atoms
746 337896 : for(unsigned a=0; a<next_res_atoms.size(); a++) {
747 158346 : string AN = pdb.getAtomName(next_res_atoms[a]);
748 168948 : if(AN=="N") { tmp_cs.bb[Nn] = next_res_atoms[a].index(); }
749 436698 : else if(AN=="H" ||AN=="HN"||(AN=="CD"&&NRES=="PRO")) { tmp_cs.bb[Hn] = next_res_atoms[a].index(); }
750 147744 : else if(AN=="CA") { tmp_cs.bb[CAn] = next_res_atoms[a].index(); }
751 370800 : else if(AN=="HA"||AN=="HA1"||AN=="HA3") { tmp_cs.bb[HAn] = next_res_atoms[a].index(); }
752 126540 : else if(AN=="C" ) { tmp_cs.bb[Cn] = next_res_atoms[a].index(); }
753 : }
754 :
755 : // set sidechain atoms
756 21204 : vector<string> sc_atm = side_chain_atoms(RES);
757 :
758 271566 : for(unsigned sc=0; sc<sc_atm.size(); sc++) {
759 4871934 : for(unsigned aa=0; aa<res_atoms.size(); aa++) {
760 4741452 : if(pdb.getAtomName(res_atoms[aa])==sc_atm[sc]) {
761 198324 : tmp_cs.side_chain.push_back(res_atoms[aa].index());
762 : }
763 : }
764 : }
765 :
766 : // find atoms for extra distances
767 296856 : const string atomsP1[] = {"H", "H", "H", "C", "C", "C", "O", "O", "O", "N", "N", "N", "O", "O", "O", "N", "N", "N", "CG", "CG", "CG", "CG", "CG", "CG", "CG", "CA"};
768 10602 : const int resOffsetP1[] = { 0, 0, 0, -1, -1, -1, 0, 0, 0, 1, 1, 1, -1, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, -1, 1, -1};
769 :
770 296856 : const string atomsP2[] = {"HA", "C", "CB", "HA", "C", "CB", "HA", "N", "CB", "HA", "N", "CB", "HA", "N", "CB", "HA", "N", "CB", "HA", "N", "C", "C", "N", "CA", "CA", "CA"};
771 10602 : const int resOffsetP2[] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, -1, -1, -1, -1, -1, 0, 0, 0, -1, 1, 0, 0, 1};
772 :
773 286254 : for(unsigned q=0; q<db.get_numXtraDists()-1; q++) {
774 : vector<AtomNumber> at1;
775 275652 : if(resOffsetP1[q]== 0) at1 = res_atoms;
776 275652 : if(resOffsetP1[q]==-1) at1 = prev_res_atoms;
777 275652 : if(resOffsetP1[q]==+1) at1 = next_res_atoms;
778 :
779 : vector<AtomNumber> at2;
780 275652 : if(resOffsetP2[q]== 0) at2 = res_atoms;
781 275652 : if(resOffsetP2[q]==-1) at2 = prev_res_atoms;
782 275652 : if(resOffsetP2[q]==+1) at2 = next_res_atoms;
783 :
784 275652 : int tmp1 = -1;
785 4395132 : for(unsigned a=0; a<at1.size(); a++) {
786 2181708 : string name = pdb.getAtomName(at1[a]);
787 2181708 : xdist_name_map(name);
788 :
789 2181708 : if(name==atomsP1[q]) {
790 259794 : tmp1 = at1[a].index();
791 : break;
792 : }
793 : }
794 :
795 275652 : int tmp2 = -1;
796 2855376 : for(unsigned a=0; a<at2.size(); a++) {
797 1418076 : string name = pdb.getAtomName(at2[a]);
798 1418076 : xdist_name_map(name);
799 :
800 1418076 : if(name==atomsP2[q]) {
801 266040 : tmp2 = at2[a].index();
802 : break;
803 : }
804 : }
805 :
806 275652 : tmp_cs.xd1.push_back(tmp1);
807 275652 : tmp_cs.xd2.push_back(tmp2);
808 : }
809 :
810 : // ready to add a new chemical shifts
811 21204 : tmp_cs.csatoms = 1 + 16 + tmp_cs.side_chain.size() + 2*tmp_cs.xd1.size();
812 20556 : if(tmp_cs.res_name!="ALA"&&tmp_cs.res_name!="GLY") tmp_cs.csatoms += 2;
813 10602 : chemicalshifts.push_back(tmp_cs);
814 : }
815 :
816 216 : in.close();
817 : }
818 :
819 : // this assigns an atom-type to each atom of the pdb
820 18 : void CS2Backbone::init_types(const PDB &pdb) {
821 : enum atom_t {D_C, D_H, D_N, D_O, D_S, D_C2, D_N2, D_O2};
822 18 : vector<AtomNumber> aa = pdb.getAtomNumbers();
823 94050 : for(unsigned i=0; i<aa.size(); i++) {
824 47016 : unsigned frag = pdb.getResidueNumber(aa[i]);
825 47016 : string fragName = pdb.getResidueName(aa[i]);
826 47016 : string atom_name = pdb.getAtomName(aa[i]);
827 47016 : char atom_type = atom_name[0];
828 51282 : if(isdigit(atom_name[0])) atom_type = atom_name[1];
829 47016 : res_num.push_back(frag);
830 47016 : unsigned t = 0;
831 47016 : if (!isSP2(fragName, atom_name)) {
832 36936 : if (atom_type == 'C') t = D_C;
833 27918 : else if (atom_type == 'O') t = D_O;
834 27450 : else if (atom_type == 'H') t = D_H;
835 4194 : else if (atom_type == 'N') t = D_N;
836 162 : else if (atom_type == 'S') t = D_S;
837 0 : else plumed_merror("Unknown atom type: " + atom_name);
838 : } else {
839 10080 : if (atom_type == 'C') t = D_C2;
840 4104 : else if (atom_type == 'O') t = D_O2;
841 0 : else if (atom_type == 'N') t = D_N2;
842 0 : else plumed_merror("Unknown atom type: " + atom_name);
843 : }
844 47016 : type.push_back(t);
845 : }
846 18 : }
847 :
848 18 : void CS2Backbone::init_rings(const PDB &pdb)
849 : {
850 18 : const string pheTyr_n[] = {"CG","CD1","CE1","CZ","CE2","CD2"};
851 144 : const string trp1_n[] = {"CD2","CE2","CZ2","CH2","CZ3","CE3"};
852 126 : const string trp2_n[] = {"CG","CD1","NE1","CE2","CD2"};
853 126 : const string his_n[] = {"CG","ND1","CD2","CE1","NE2"};
854 :
855 : // number of chains
856 18 : vector<string> chains;
857 18 : pdb.getChainNames( chains );
858 : unsigned total_rings_atoms = 0;
859 :
860 : // cycle over chains
861 90 : for(unsigned i=0; i<chains.size(); i++) {
862 : unsigned start, end;
863 : string errmsg;
864 36 : pdb.getResidueRange( chains[i], start, end, errmsg );
865 : // cycle over residues
866 3168 : for(unsigned res=start; res<end; res++) {
867 3132 : string frg = pdb.getResidueName(res, chains[i]);
868 11574 : if(!((frg=="PHE")||(frg=="TYR")||(frg=="TRP")||
869 8370 : (frg=="HIS")||(frg=="HIP")||(frg=="HID")||
870 5580 : (frg=="HIE")||(frg=="HSD")||(frg=="HSE")||
871 5922 : (frg=="HSP"))) continue;
872 :
873 342 : vector<AtomNumber> frg_atoms = pdb.getAtomsInResidue(res,chains[i]);
874 :
875 396 : if(frg=="PHE"||frg=="TYR") {
876 324 : RingInfo ri;
877 13680 : for(unsigned a=0; a<frg_atoms.size(); a++) {
878 : unsigned atm = frg_atoms[a].index();
879 38808 : for(unsigned aa=0; aa<6; aa++) {
880 102708 : if(pdb.getAtomName(frg_atoms[a])==pheTyr_n[aa]) {
881 1944 : ri.atom[aa] = atm;
882 1944 : break;
883 : }
884 : }
885 : }
886 324 : ri.numAtoms = 6;
887 324 : total_rings_atoms += 6;
888 324 : if(frg=="PHE") ri.rtype = RingInfo::R_PHE;
889 324 : if(frg=="TYR") ri.rtype = RingInfo::R_TYR;
890 324 : ringInfo.push_back(ri);
891 :
892 18 : } else if(frg=="TRP") {
893 : //First ring
894 18 : RingInfo ri;
895 900 : for(unsigned a=0; a<frg_atoms.size(); a++) {
896 : unsigned atm = frg_atoms[a].index();
897 2646 : for(unsigned aa=0; aa<6; aa++) {
898 6966 : if(pdb.getAtomName(frg_atoms[a])==trp1_n[aa]) {
899 108 : ri.atom[aa] = atm;
900 108 : break;
901 : }
902 : }
903 : }
904 18 : ri.numAtoms = 6;
905 : total_rings_atoms += 6;
906 18 : ri.rtype = RingInfo::R_TRP1;
907 18 : ringInfo.push_back(ri);
908 : //Second Ring
909 18 : RingInfo ri2;
910 900 : for(unsigned a=0; a<frg_atoms.size(); a++) {
911 : unsigned atm = frg_atoms[a].index();
912 2322 : for(unsigned aa=0; aa<5; aa++) {
913 5940 : if(pdb.getAtomName(frg_atoms[a])==trp2_n[aa]) {
914 90 : ri2.atom[aa] = atm;
915 90 : break;
916 : }
917 : }
918 : }
919 18 : ri2.numAtoms = 5;
920 18 : total_rings_atoms += 3;
921 18 : ri2.rtype = RingInfo::R_TRP2;
922 18 : ringInfo.push_back(ri2);
923 :
924 0 : } else if((frg=="HIS")||(frg=="HIP")||(frg=="HID")||
925 0 : (frg=="HIE")||(frg=="HSD")||(frg=="HSE")||
926 : (frg=="HSP")) {//HIS case
927 0 : RingInfo ri;
928 0 : for(unsigned a=0; a<frg_atoms.size(); a++) {
929 : unsigned atm = frg_atoms[a].index();
930 0 : for(unsigned aa=0; aa<5; aa++) {
931 0 : if(pdb.getAtomName(frg_atoms[a])==his_n[aa]) {
932 0 : ri.atom[aa] = atm;
933 0 : break;
934 : }
935 : }
936 : }
937 0 : ri.numAtoms = 5;
938 0 : total_rings_atoms += 3;
939 0 : ri.rtype = RingInfo::R_HIS;
940 0 : ringInfo.push_back(ri);
941 : } else {
942 0 : plumed_merror("Unknown Ring Fragment: " + frg);
943 : }
944 : }
945 : }
946 :
947 21348 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) chemicalshifts[cs].csatoms += total_rings_atoms;
948 18 : }
949 :
950 18 : void CS2Backbone::calculate()
951 : {
952 18 : if(pbc) makeWhole();
953 18 : if(getExchangeStep()) box_count=0;
954 18 : if(box_count==0) update_neighb();
955 18 : compute_ring_parameters();
956 :
957 18 : vector<double> camshift_sigma2(6);
958 18 : camshift_sigma2[0] = 0.08; // HA
959 18 : camshift_sigma2[1] = 0.30; // HN
960 18 : camshift_sigma2[2] = 9.00; // NH
961 18 : camshift_sigma2[3] = 1.30; // CA
962 18 : camshift_sigma2[4] = 1.56; // CB
963 18 : camshift_sigma2[5] = 1.70; // CO
964 :
965 : vector<Vector> cs_derivs;
966 : vector<Vector> aa_derivs;
967 : vector<unsigned> cs_atoms;
968 : vector<double> all_shifts;
969 :
970 36 : cs_derivs.resize(chemicalshifts.size()*max_cs_atoms,Vector(0,0,0));
971 36 : cs_atoms.resize(chemicalshifts.size()*max_cs_atoms,0);
972 36 : all_shifts.resize(chemicalshifts.size(),0);
973 40 : if(camshift||getDoScore()) aa_derivs.resize(getNumberOfAtoms(),Vector(0,0,0));
974 :
975 18 : unsigned stride = comm.Get_size();
976 18 : unsigned rank = comm.Get_rank();
977 18 : if(serial) {
978 : stride = 1;
979 : rank = 0;
980 : }
981 :
982 18 : unsigned nt=OpenMP::getNumThreads();
983 36 : if(nt*stride*2>chemicalshifts.size()) nt=1;
984 :
985 : // a single loop over all chemical shifts
986 54 : #pragma omp parallel num_threads(nt)
987 : {
988 36 : #pragma omp for schedule(dynamic)
989 36 : for(unsigned cs=rank; cs<chemicalshifts.size(); cs+=stride) {
990 5870 : const unsigned kdx=cs*max_cs_atoms;
991 5870 : const ChemicalShift *myfrag = &chemicalshifts[cs];
992 5870 : const unsigned aa_kind = myfrag->res_kind;
993 5870 : const unsigned at_kind = myfrag->atm_kind;
994 :
995 11740 : double shift = db.CONSTAAPREV(aa_kind,at_kind)[myfrag->res_type_prev] +
996 5870 : db.CONSTAACURR(aa_kind,at_kind)[myfrag->res_type_curr] +
997 5870 : db.CONSTAANEXT(aa_kind,at_kind)[myfrag->res_type_next];
998 :
999 5870 : const unsigned ipos = myfrag->ipos;
1000 11740 : cs_atoms[kdx+0] = ipos;
1001 : unsigned atom_counter = 1;
1002 :
1003 : //BACKBONE (PREV CURR NEXT)
1004 5870 : const double * CONST_BB2 = db.CONST_BB2(aa_kind,at_kind);
1005 : const unsigned bbsize = 16;
1006 99849 : for(unsigned q=0; q<bbsize; q++) {
1007 93961 : const double cb2q = CONST_BB2[q];
1008 110892 : if(cb2q==0.) continue;
1009 76994 : const unsigned jpos = myfrag->bb[q];
1010 76994 : if(ipos==jpos) continue;
1011 231090 : const Vector distance = delta(getPosition(jpos),getPosition(ipos));
1012 77075 : const double d = distance.modulo();
1013 77171 : const double fact = cb2q/d;
1014 :
1015 77171 : shift += cb2q*d;
1016 77171 : const Vector der = fact*distance;
1017 :
1018 154582 : cs_derivs[kdx+0] += der;
1019 154576 : cs_derivs[kdx+q+atom_counter] = -der;
1020 154096 : cs_atoms[kdx+q+atom_counter] = jpos;
1021 : }
1022 :
1023 : atom_counter += bbsize;
1024 :
1025 : //DIHEDRAL ANGLES
1026 5888 : const double *CO_DA = db.CO_DA(aa_kind,at_kind);
1027 : //Phi
1028 : {
1029 17664 : const Vector d0 = delta(getPosition(myfrag->bb[Nc]), getPosition(myfrag->bb[Cp]));
1030 17664 : const Vector d1 = delta(getPosition(myfrag->bb[CAc]), getPosition(myfrag->bb[Nc]));
1031 17667 : const Vector d2 = delta(getPosition(myfrag->bb[Cc]), getPosition(myfrag->bb[CAc]));
1032 : Torsion t;
1033 5889 : Vector dd0, dd1, dd2;
1034 5890 : const double t_phi = t.compute(d0,d1,d2,dd0,dd1,dd2);
1035 5889 : const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,0);
1036 5889 : const double val1 = 3.*t_phi+PARS_DA[3];
1037 5889 : const double val2 = t_phi+PARS_DA[4];
1038 5889 : shift += CO_DA[0]*(PARS_DA[0]*cos(val1)+PARS_DA[1]*cos(val2)+PARS_DA[2]);
1039 5889 : const double fact = -CO_DA[0]*(+3.*PARS_DA[0]*sin(val1)+PARS_DA[1]*sin(val2));
1040 :
1041 11779 : cs_derivs[kdx+Cp+1] += fact*dd0;
1042 11779 : cs_derivs[kdx+Nc+1] += fact*(dd1-dd0);
1043 11777 : cs_derivs[kdx+CAc+1]+= fact*(dd2-dd1);
1044 11779 : cs_derivs[kdx+Cc+1] += -fact*dd2;
1045 11780 : cs_atoms[kdx+Cp+1] = myfrag->bb[Cp];
1046 11780 : cs_atoms[kdx+Nc+1] = myfrag->bb[Nc];
1047 11780 : cs_atoms[kdx+CAc+1]= myfrag->bb[CAc];
1048 11780 : cs_atoms[kdx+Cc+1] = myfrag->bb[Cc];
1049 : }
1050 :
1051 : //Psi
1052 : {
1053 17670 : const Vector d0 = delta(getPosition(myfrag->bb[CAc]), getPosition(myfrag->bb[Nc]));
1054 17655 : const Vector d1 = delta(getPosition(myfrag->bb[Cc]), getPosition(myfrag->bb[CAc]));
1055 17670 : const Vector d2 = delta(getPosition(myfrag->bb[Nn]), getPosition(myfrag->bb[Cc]));
1056 : Torsion t;
1057 5890 : Vector dd0, dd1, dd2;
1058 5890 : const double t_psi = t.compute(d0,d1,d2,dd0,dd1,dd2);
1059 5890 : const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,1);
1060 5890 : const double val1 = 3.*t_psi+PARS_DA[3];
1061 5890 : const double val2 = t_psi+PARS_DA[4];
1062 5890 : shift += CO_DA[1]*(PARS_DA[0]*cos(val1)+PARS_DA[1]*cos(val2)+PARS_DA[2]);
1063 5890 : const double fact = -CO_DA[1]*(+3.*PARS_DA[0]*sin(val1)+PARS_DA[1]*sin(val2));
1064 :
1065 11779 : cs_derivs[kdx+Nc+1] += fact*dd0;
1066 11776 : cs_derivs[kdx+CAc+1] += fact*(dd1-dd0);
1067 11780 : cs_derivs[kdx+Cc+1] += fact*(dd2-dd1);
1068 11780 : cs_derivs[kdx+Nn+1] += -fact*dd2;
1069 12524 : cs_atoms[kdx+Nc+1] = myfrag->bb[Nc];
1070 12524 : cs_atoms[kdx+CAc+1]= myfrag->bb[CAc];
1071 12524 : cs_atoms[kdx+Cc+1] = myfrag->bb[Cc];
1072 12524 : cs_atoms[kdx+Nn+1] = myfrag->bb[Nn];
1073 : }
1074 :
1075 : //Chi
1076 6262 : if(myfrag->has_chi1) {
1077 14088 : const Vector d0 = delta(getPosition(myfrag->bb[CAc]), getPosition(myfrag->bb[Nc]));
1078 14082 : const Vector d1 = delta(getPosition(myfrag->bb[CBc]), getPosition(myfrag->bb[CAc]));
1079 14094 : const Vector d2 = delta(getPosition(myfrag->bb[CGc]), getPosition(myfrag->bb[CBc]));
1080 : Torsion t;
1081 4700 : Vector dd0, dd1, dd2;
1082 4700 : const double t_chi1 = t.compute(d0,d1,d2,dd0,dd1,dd2);
1083 4700 : const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,2);
1084 4700 : const double val1 = 3.*t_chi1+PARS_DA[3];
1085 4700 : const double val2 = t_chi1+PARS_DA[4];
1086 4700 : shift += CO_DA[2]*(PARS_DA[0]*cos(val1)+PARS_DA[1]*cos(val2)+PARS_DA[2]);
1087 4700 : const double fact = -CO_DA[2]*(+3.*PARS_DA[0]*sin(val1)+PARS_DA[1]*sin(val2));
1088 :
1089 9400 : cs_derivs[kdx+Nc+1] += fact*dd0;
1090 9400 : cs_derivs[kdx+CAc+1] += fact*(dd1-dd0);
1091 9400 : cs_derivs[kdx+CBc+1] += fact*(dd2-dd1);
1092 9400 : cs_derivs[kdx+CGc+1] += -fact*dd2;
1093 9400 : cs_atoms[kdx+Nc+1] = myfrag->bb[Nc];
1094 9400 : cs_atoms[kdx+CAc+1] = myfrag->bb[CAc];
1095 9400 : cs_atoms[kdx+CBc+1] = myfrag->bb[CBc];
1096 9400 : cs_atoms[kdx+CGc+1] = myfrag->bb[CGc];
1097 :
1098 : atom_counter += 2;
1099 : }
1100 : //END OF DIHE
1101 :
1102 : //SIDE CHAIN
1103 6266 : const double * CONST_SC2 = db.CONST_SC2(aa_kind,at_kind,myfrag->res_type_curr);
1104 6266 : const unsigned sidsize = myfrag->side_chain.size();
1105 61319 : for(unsigned q=0; q<sidsize; q++) {
1106 55061 : const double cs2q = CONST_SC2[q];
1107 86520 : if(cs2q==0.) continue;
1108 23599 : const unsigned jpos = myfrag->side_chain[q];
1109 23599 : if(ipos==jpos) continue;
1110 70806 : const Vector distance = delta(getPosition(jpos),getPosition(ipos));
1111 23605 : const double d = distance.modulo();
1112 23604 : const double fact = cs2q/d;
1113 :
1114 23604 : shift += cs2q*d;
1115 23604 : const Vector der = fact*distance;
1116 47238 : cs_derivs[kdx+0] += der;
1117 47240 : cs_derivs[kdx+q+atom_counter] = -der;
1118 47188 : cs_atoms[kdx+q+atom_counter] = jpos;
1119 : }
1120 :
1121 6258 : atom_counter += sidsize;
1122 :
1123 : //EXTRA DIST
1124 6258 : const double * CONST_XD = db.CONST_XD(aa_kind,at_kind);
1125 6258 : const unsigned xdsize=myfrag->xd1.size();
1126 158951 : for(unsigned q=0; q<xdsize; q++) {
1127 152890 : const double cxdq = CONST_XD[q];
1128 167040 : if(cxdq==0.) continue;
1129 290100 : if(myfrag->xd1[q]==-1||myfrag->xd2[q]==-1) continue;
1130 277480 : const Vector distance = delta(getPosition(myfrag->xd1[q]),getPosition(myfrag->xd2[q]));
1131 138767 : const double d = distance.modulo();
1132 138912 : const double fact = cxdq/d;
1133 :
1134 138912 : shift += cxdq*d;
1135 138912 : const Vector der = fact*distance;
1136 277940 : cs_derivs[kdx+2*q+atom_counter ] = der;
1137 277940 : cs_derivs[kdx+2*q+atom_counter+1] = -der;
1138 277086 : cs_atoms[kdx+2*q+atom_counter] = myfrag->xd2[q];
1139 277086 : cs_atoms[kdx+2*q+atom_counter+1] = myfrag->xd1[q];
1140 : }
1141 :
1142 6061 : atom_counter += 2*xdsize;
1143 :
1144 : //RINGS
1145 6061 : const double *rc = db.CO_RING(aa_kind,at_kind);
1146 6061 : const unsigned rsize = ringInfo.size();
1147 : // cycle over the list of rings
1148 123749 : for(unsigned q=0; q<rsize; q++) {
1149 : // compute angle from ring middle point to current atom position
1150 : // get distance vector from query atom to ring center and normal vector to ring plane
1151 235360 : const Vector n = ringInfo[q].normVect;
1152 117680 : const double nL = ringInfo[q].lengthNV;
1153 117680 : const double inL2 = ringInfo[q].lengthN2;
1154 :
1155 235360 : const Vector d = delta(ringInfo[q].position, getPosition(ipos));
1156 117715 : const double dL2 = d.modulo2();
1157 117793 : double dL = sqrt(dL2);
1158 117793 : const double idL3 = 1./(dL2*dL);
1159 :
1160 117793 : const double dn = dotProduct(d,n);
1161 117799 : const double dn2 = dn*dn;
1162 117799 : const double dLnL = dL*nL;
1163 117799 : const double dL_nL = dL/nL;
1164 :
1165 117799 : const double ang2 = dn2*inL2/dL2;
1166 117799 : const double u = 1.-3.*ang2;
1167 117799 : const double cc = rc[ringInfo[q].rtype];
1168 :
1169 117799 : shift += cc*u*idL3;
1170 :
1171 117799 : const double fUU = -6.*dn*inL2;
1172 117799 : const double fUQ = fUU/dL;
1173 117799 : const Vector gradUQ = fUQ*(dL2*n - dn*d);
1174 117796 : const Vector gradVQ = (3.*dL*u)*d;
1175 :
1176 117785 : const double fact = cc*idL3*idL3;
1177 235573 : cs_derivs[kdx+0] += fact*(gradUQ - gradVQ);
1178 :
1179 117789 : const double fU = fUU/nL;
1180 : double OneOverN = 1./6.;
1181 117789 : if(ringInfo[q].numAtoms==5) OneOverN=1./3.;
1182 117789 : const Vector factor2 = OneOverN*n;
1183 117784 : const Vector factor4 = (OneOverN/dL_nL)*d;
1184 :
1185 117787 : const Vector gradV = -OneOverN*gradVQ;
1186 :
1187 118540 : if(ringInfo[q].numAtoms==6) {
1188 : // update forces on ring atoms
1189 1445624 : for(unsigned at=0; at<6; at++) {
1190 667339 : const Vector ab = crossProduct(d,ringInfo[q].g[at]);
1191 669051 : const Vector c = crossProduct(n,ringInfo[q].g[at]);
1192 670978 : const Vector factor3 = 0.5*dL_nL*c;
1193 671328 : const Vector factor1 = 0.5*ab;
1194 671133 : const Vector gradU = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );
1195 1340362 : cs_derivs[kdx+at+atom_counter] = fact*(gradU - gradV);
1196 1332974 : cs_atoms[kdx+at+atom_counter] = ringInfo[q].atom[at];
1197 : }
1198 111798 : atom_counter += 6;
1199 : } else {
1200 41226 : for(unsigned at=0; at<3; at++) {
1201 17668 : const Vector ab = crossProduct(d,ringInfo[q].g[at]);
1202 17670 : const Vector c = crossProduct(n,ringInfo[q].g[at]);
1203 17670 : const Vector factor3 = dL_nL*c;
1204 17669 : const Vector factor1 = ab;
1205 17669 : const Vector gradU = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );
1206 35340 : cs_derivs[kdx+at+atom_counter] = fact*(gradU - gradV);
1207 : }
1208 11780 : cs_atoms[kdx+atom_counter] = ringInfo[q].atom[0];
1209 11780 : cs_atoms[kdx+atom_counter+1] = ringInfo[q].atom[2];
1210 11780 : cs_atoms[kdx+atom_counter+2] = ringInfo[q].atom[3];
1211 5890 : atom_counter += 3;
1212 : }
1213 : }
1214 : //END OF RINGS
1215 :
1216 : //NON BOND
1217 6069 : const double * CONST_CO_SPHERE3 = db.CO_SPHERE(aa_kind,at_kind,0);
1218 6069 : const double * CONST_CO_SPHERE = db.CO_SPHERE(aa_kind,at_kind,1);
1219 6069 : const unsigned boxsize = myfrag->box_nb.size();
1220 250854 : for(unsigned q=0; q<boxsize; q++) {
1221 489928 : const unsigned jpos = myfrag->box_nb[q];
1222 734892 : const Vector distance = delta(getPosition(jpos),getPosition(ipos));
1223 245094 : const double d2 = distance.modulo2();
1224 :
1225 244869 : if(d2<cutOffDist2) {
1226 108356 : double factor1 = sqrt(d2);
1227 108356 : double dfactor1 = 1./factor1;
1228 108356 : double factor3 = dfactor1*dfactor1*dfactor1;
1229 108356 : double dfactor3 = -3.*factor3*dfactor1*dfactor1;
1230 :
1231 108356 : if(d2>cutOnDist2) {
1232 101573 : const double af = cutOffDist2 - d2;
1233 101573 : const double bf = cutOffDist2 - 3.*cutOnDist2 + 2.*d2;
1234 101573 : const double cf = invswitch*af;
1235 101573 : const double df = cf*af*bf;
1236 101573 : factor1 *= df;
1237 101573 : factor3 *= df;
1238 :
1239 101573 : const double d4 = d2*d2;
1240 101573 : const double af1 = 15.*cutOnDist2*d2;
1241 101573 : const double bf1 = -14.*d4;
1242 101573 : const double cf1 = -3.*cutOffDist2*cutOnDist2 + cutOffDist2*d2;
1243 101573 : const double df1 = af1+bf1+cf1;
1244 101573 : dfactor1 *= cf*(cutOffDist4+df1);
1245 :
1246 : const double af3 = +2.*cutOffDist2*cutOnDist2;
1247 101573 : const double bf3 = d2*(cutOffDist2+cutOnDist2);
1248 101573 : const double cf3 = -2.*d4;
1249 101573 : const double df3 = (af3+bf3+cf3)*d2;
1250 101573 : dfactor3 *= invswitch*(cutMixed+df3);
1251 : }
1252 :
1253 216712 : const unsigned t = type[jpos];
1254 108356 : shift += factor1*CONST_CO_SPHERE[t] + factor3*CONST_CO_SPHERE3[t] ;
1255 108356 : const double fact = dfactor1*CONST_CO_SPHERE[t]+dfactor3*CONST_CO_SPHERE3[t];
1256 108356 : const Vector der = fact*distance;
1257 :
1258 216874 : cs_derivs[kdx+0] += der;
1259 216874 : cs_derivs[kdx+q+atom_counter] = -der;
1260 216544 : cs_atoms[kdx+q+atom_counter] = jpos;
1261 : }
1262 : }
1263 : //END NON BOND
1264 :
1265 : atom_counter += boxsize;
1266 11780 : all_shifts[cs] = shift;
1267 : }
1268 : }
1269 :
1270 18 : ++box_count;
1271 18 : if(box_count == box_nupdate) box_count = 0;
1272 :
1273 18 : if(!camshift) {
1274 13 : if(!serial) {
1275 13 : if(!getDoScore()) {
1276 9 : comm.Sum(&cs_derivs[0][0], 3*cs_derivs.size());
1277 9 : comm.Sum(&cs_atoms[0], cs_atoms.size());
1278 : }
1279 26 : comm.Sum(&all_shifts[0], chemicalshifts.size());
1280 : }
1281 15327 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
1282 7657 : Value *comp = chemicalshifts[cs].comp;
1283 7657 : comp->set(all_shifts[cs]);
1284 10013 : if(getDoScore()) setCalcData(cs, all_shifts[cs]);
1285 : else {
1286 5301 : const unsigned kdx=cs*max_cs_atoms;
1287 5301 : Tensor csvirial;
1288 2540254 : for(unsigned i=0; i<chemicalshifts[cs].totcsatoms; i++) {
1289 2529652 : setAtomsDerivatives(comp,cs_atoms[kdx+i],cs_derivs[kdx+i]);
1290 2529652 : csvirial-=Tensor(getPosition(cs_atoms[kdx+i]),cs_derivs[kdx+i]);
1291 : }
1292 5301 : setBoxDerivatives(comp,csvirial);
1293 : }
1294 : }
1295 31 : if(!getDoScore()) return;
1296 : }
1297 :
1298 9 : double score = 0.;
1299 :
1300 : /* Metainference */
1301 9 : if(getDoScore()) {
1302 4 : score = getScore();
1303 2364 : for(unsigned cs=rank; cs<chemicalshifts.size(); cs+=stride) {
1304 1178 : const unsigned kdx=cs*max_cs_atoms;
1305 : const double fact = getMetaDer(cs);
1306 564430 : for(unsigned i=0; i<chemicalshifts[cs].totcsatoms; i++) {
1307 1124148 : aa_derivs[cs_atoms[kdx+i]] += cs_derivs[kdx+i]*fact;
1308 : }
1309 : }
1310 : }
1311 :
1312 : /* camshift */
1313 9 : if(camshift) {
1314 3539 : for(unsigned cs=rank; cs<chemicalshifts.size(); cs+=stride) {
1315 1767 : const unsigned kdx=cs*max_cs_atoms;
1316 5301 : score += (all_shifts[cs] - chemicalshifts[cs].exp_cs)*(all_shifts[cs] - chemicalshifts[cs].exp_cs)/camshift_sigma2[chemicalshifts[cs].atm_kind];
1317 1767 : double fact = 2.0*(all_shifts[cs] - chemicalshifts[cs].exp_cs)/camshift_sigma2[chemicalshifts[cs].atm_kind];
1318 846964 : for(unsigned i=0; i<chemicalshifts[cs].totcsatoms; i++) {
1319 1686860 : aa_derivs[cs_atoms[kdx+i]] += cs_derivs[kdx+i]*fact;
1320 : }
1321 : }
1322 : }
1323 :
1324 9 : if(!serial) {
1325 9 : comm.Sum(&aa_derivs[0][0], 3*aa_derivs.size());
1326 9 : if(camshift) comm.Sum(&score, 1);
1327 : }
1328 :
1329 9 : Tensor virial;
1330 26138 : for(unsigned i=rank; i<getNumberOfAtoms(); i+=stride) {
1331 39180 : virial += Tensor(getPosition(i), aa_derivs[i]);
1332 : }
1333 :
1334 9 : if(!serial) {
1335 9 : comm.Sum(&virial[0][0], 9);
1336 : }
1337 :
1338 : /* calculate final derivatives */
1339 : Value* val;
1340 9 : if(getDoScore()) {
1341 8 : val=getPntrToComponent("score");
1342 4 : setScore(score);
1343 : } else {
1344 5 : val=getPntrToValue();
1345 5 : setValue(score);
1346 : }
1347 :
1348 : /* at this point we cycle over all atoms */
1349 47034 : for(unsigned i=0; i<getNumberOfAtoms(); i++) setAtomsDerivatives(val, i, aa_derivs[i]);
1350 9 : setBoxDerivatives(val,-virial);
1351 : }
1352 :
1353 18 : void CS2Backbone::update_neighb() {
1354 18 : max_cs_atoms=0;
1355 : // cycle over chemical shifts
1356 21240 : for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
1357 : const unsigned boxsize = getNumberOfAtoms();
1358 : chemicalshifts[cs].box_nb.clear();
1359 10602 : chemicalshifts[cs].box_nb.reserve(150);
1360 21204 : const unsigned res_curr = res_num[chemicalshifts[cs].ipos];
1361 27703026 : for(unsigned bat=0; bat<boxsize; bat++) {
1362 55384848 : const unsigned res_dist = abs(static_cast<int>(res_curr-res_num[bat]));
1363 28171332 : if(res_dist<2) continue;
1364 81640548 : const Vector distance = delta(getPosition(bat),getPosition(chemicalshifts[cs].ipos));
1365 27213516 : const double d2=distance.modulo2();
1366 27655114 : if(d2<cutOffNB2) chemicalshifts[cs].box_nb.push_back(bat);
1367 : }
1368 21204 : chemicalshifts[cs].totcsatoms = chemicalshifts[cs].csatoms + chemicalshifts[cs].box_nb.size();
1369 10602 : if(chemicalshifts[cs].totcsatoms>max_cs_atoms) max_cs_atoms = chemicalshifts[cs].totcsatoms;
1370 : }
1371 18 : }
1372 :
1373 18 : void CS2Backbone::compute_ring_parameters() {
1374 756 : for(unsigned i=0; i<ringInfo.size(); i++) {
1375 360 : const unsigned size = ringInfo[i].numAtoms;
1376 360 : if(size==6) {
1377 1026 : ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[4]),getPosition(ringInfo[i].atom[2]));
1378 1026 : ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[5]),getPosition(ringInfo[i].atom[3]));
1379 1026 : ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[4]));
1380 1026 : ringInfo[i].g[3] = delta(getPosition(ringInfo[i].atom[1]),getPosition(ringInfo[i].atom[5]));
1381 1026 : ringInfo[i].g[4] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));
1382 1026 : ringInfo[i].g[5] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[1]));
1383 342 : vector<Vector> a(6);
1384 684 : a[0] = getPosition(ringInfo[i].atom[0]);
1385 : // ring center
1386 342 : Vector midP = a[0];
1387 2052 : for(unsigned j=1; j<size; j++) {
1388 5130 : a[j] = getPosition(ringInfo[i].atom[j]);
1389 1710 : midP += a[j];
1390 : }
1391 342 : ringInfo[i].position = midP/6.;
1392 : // compute normal vector to plane
1393 684 : Vector n1 = crossProduct(delta(a[0],a[4]), delta(a[0],a[2]));
1394 684 : Vector n2 = crossProduct(delta(a[3],a[1]), delta(a[3],a[5]));
1395 342 : ringInfo[i].normVect = 0.5*(n1 + n2);
1396 : } else {
1397 54 : ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[2]));
1398 54 : ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[3]));
1399 54 : ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));
1400 18 : vector<Vector> a(size);
1401 108 : for(unsigned j=0; j<size; j++) {
1402 270 : a[j] = getPosition(ringInfo[i].atom[j]);
1403 : }
1404 : // ring center
1405 18 : ringInfo[i].position = (a[0]+a[2]+a[3])/3.;
1406 : // ring plane normal vector
1407 36 : ringInfo[i].normVect = crossProduct(delta(a[0],a[3]), delta(a[0],a[2]));
1408 :
1409 : }
1410 : // calculate squared length and length of normal vector
1411 360 : ringInfo[i].lengthN2 = 1./ringInfo[i].normVect.modulo2();
1412 360 : ringInfo[i].lengthNV = 1./sqrt(ringInfo[i].lengthN2);
1413 : }
1414 18 : }
1415 :
1416 31806 : CS2Backbone::aa_t CS2Backbone::frag2enum(const string &aa) {
1417 : aa_t type = ALA;
1418 31806 : if (aa == "ALA") type = ALA;
1419 29934 : else if (aa == "ARG") type = ARG;
1420 28548 : else if (aa == "ASN") type = ASN;
1421 26910 : else if (aa == "ASP") type = ASP;
1422 25380 : else if (aa == "ASH") type = ASP;
1423 25380 : else if (aa == "CYS") type = CYS;
1424 24858 : else if (aa == "CYM") type = CYS;
1425 24858 : else if (aa == "GLN") type = GLN;
1426 24390 : else if (aa == "GLU") type = GLU;
1427 22068 : else if (aa == "GLH") type = GLU;
1428 22068 : else if (aa == "GLY") type = GLY;
1429 16974 : else if (aa == "HIS") type = HIS;
1430 16974 : else if (aa == "HSE") type = HIS;
1431 16974 : else if (aa == "HIE") type = HIS;
1432 16974 : else if (aa == "HSP") type = HIS;
1433 16974 : else if (aa == "HIP") type = HIS;
1434 16974 : else if (aa == "HSD") type = HIS;
1435 16974 : else if (aa == "HID") type = HIS;
1436 16974 : else if (aa == "ILE") type = ILE;
1437 15174 : else if (aa == "LEU") type = LEU;
1438 13536 : else if (aa == "LYS") type = LYS;
1439 10746 : else if (aa == "MET") type = MET;
1440 9936 : else if (aa == "PHE") type = PHE;
1441 6876 : else if (aa == "PRO") type = PRO;
1442 5940 : else if (aa == "SER") type = SER;
1443 4302 : else if (aa == "THR") type = THR;
1444 2196 : else if (aa == "TRP") type = TRP;
1445 1980 : else if (aa == "TYR") type = TYR;
1446 1602 : else if (aa == "VAL") type = VAL;
1447 0 : else if (aa == "UNK") type = UNK;
1448 0 : else plumed_merror("Error converting string " + aa + " into amino acid index: not a valid 3-letter code");
1449 31806 : return type;
1450 : }
1451 :
1452 10602 : vector<string> CS2Backbone::side_chain_atoms(const string &s) {
1453 : vector<string> sc;
1454 :
1455 10602 : if(s=="ALA") {
1456 1296 : sc.push_back( "CB" );
1457 1296 : sc.push_back( "HB1" );
1458 1296 : sc.push_back( "HB2" );
1459 1296 : sc.push_back( "HB3" );
1460 648 : return sc;
1461 9954 : } else if(s=="ARG") {
1462 936 : sc.push_back( "CB" );
1463 936 : sc.push_back( "CG" );
1464 936 : sc.push_back( "CD" );
1465 936 : sc.push_back( "NE" );
1466 936 : sc.push_back( "CZ" );
1467 936 : sc.push_back( "NH1" );
1468 936 : sc.push_back( "NH2" );
1469 936 : sc.push_back( "NH3" );
1470 936 : sc.push_back( "HB1" );
1471 936 : sc.push_back( "HB2" );
1472 936 : sc.push_back( "HB3" );
1473 936 : sc.push_back( "HG1" );
1474 936 : sc.push_back( "HG2" );
1475 936 : sc.push_back( "HG3" );
1476 936 : sc.push_back( "HD1" );
1477 936 : sc.push_back( "HD2" );
1478 936 : sc.push_back( "HD3" );
1479 936 : sc.push_back( "HE" );
1480 936 : sc.push_back( "HH11" );
1481 936 : sc.push_back( "HH12" );
1482 936 : sc.push_back( "HH21" );
1483 936 : sc.push_back( "HH22" );
1484 936 : sc.push_back( "1HH1" );
1485 936 : sc.push_back( "2HH1" );
1486 936 : sc.push_back( "1HH2" );
1487 936 : sc.push_back( "2HH2" );
1488 468 : return sc;
1489 9486 : } else if(s=="ASN") {
1490 1188 : sc.push_back( "CB" );
1491 1188 : sc.push_back( "CG" );
1492 1188 : sc.push_back( "OD1" );
1493 1188 : sc.push_back( "ND2" );
1494 1188 : sc.push_back( "HB1" );
1495 1188 : sc.push_back( "HB2" );
1496 1188 : sc.push_back( "HB3" );
1497 1188 : sc.push_back( "HD21" );
1498 1188 : sc.push_back( "HD22" );
1499 1188 : sc.push_back( "1HD2" );
1500 1188 : sc.push_back( "2HD2" );
1501 594 : return sc;
1502 17226 : } else if(s=="ASP"||s=="ASH") {
1503 1116 : sc.push_back( "CB" );
1504 1116 : sc.push_back( "CG" );
1505 1116 : sc.push_back( "OD1" );
1506 1116 : sc.push_back( "OD2" );
1507 1116 : sc.push_back( "HB1" );
1508 1116 : sc.push_back( "HB2" );
1509 1116 : sc.push_back( "HB3" );
1510 558 : return sc;
1511 16668 : } else if(s=="CYS"||s=="CYM") {
1512 0 : sc.push_back( "CB" );
1513 0 : sc.push_back( "SG" );
1514 0 : sc.push_back( "HB1" );
1515 0 : sc.push_back( "HB2" );
1516 0 : sc.push_back( "HB3" );
1517 0 : sc.push_back( "HG1" );
1518 0 : sc.push_back( "HG" );
1519 0 : return sc;
1520 8334 : } else if(s=="GLN") {
1521 324 : sc.push_back( "CB" );
1522 324 : sc.push_back( "CG" );
1523 324 : sc.push_back( "CD" );
1524 324 : sc.push_back( "OE1" );
1525 324 : sc.push_back( "NE2" );
1526 324 : sc.push_back( "HB1" );
1527 324 : sc.push_back( "HB2" );
1528 324 : sc.push_back( "HB3" );
1529 324 : sc.push_back( "HG1" );
1530 324 : sc.push_back( "HG2" );
1531 324 : sc.push_back( "HG3" );
1532 324 : sc.push_back( "HE21" );
1533 324 : sc.push_back( "HE22" );
1534 324 : sc.push_back( "1HE2" );
1535 324 : sc.push_back( "2HE2" );
1536 162 : return sc;
1537 15552 : } else if(s=="GLU"||s=="GLH") {
1538 1584 : sc.push_back( "CB" );
1539 1584 : sc.push_back( "CG" );
1540 1584 : sc.push_back( "CD" );
1541 1584 : sc.push_back( "OE1" );
1542 1584 : sc.push_back( "OE2" );
1543 1584 : sc.push_back( "HB1" );
1544 1584 : sc.push_back( "HB2" );
1545 1584 : sc.push_back( "HB3" );
1546 1584 : sc.push_back( "HG1" );
1547 1584 : sc.push_back( "HG2" );
1548 1584 : sc.push_back( "HG3" );
1549 792 : return sc;
1550 7380 : } else if(s=="GLY") {
1551 2988 : sc.push_back( "HA2" );
1552 1494 : return sc;
1553 41202 : } else if(s=="HIS"||s=="HSE"||s=="HIE"||s=="HSD"||s=="HID"||s=="HIP"||s=="HSP") {
1554 0 : sc.push_back( "CB" );
1555 0 : sc.push_back( "CG" );
1556 0 : sc.push_back( "ND1" );
1557 0 : sc.push_back( "CD2" );
1558 0 : sc.push_back( "CE1" );
1559 0 : sc.push_back( "NE2" );
1560 0 : sc.push_back( "HB1" );
1561 0 : sc.push_back( "HB2" );
1562 0 : sc.push_back( "HB3" );
1563 0 : sc.push_back( "HD1" );
1564 0 : sc.push_back( "HD2" );
1565 0 : sc.push_back( "HE1" );
1566 0 : sc.push_back( "HE2" );
1567 0 : return sc;
1568 5886 : } else if(s=="ILE") {
1569 1080 : sc.push_back( "CB" );
1570 1080 : sc.push_back( "CG1" );
1571 1080 : sc.push_back( "CG2" );
1572 1080 : sc.push_back( "CD" );
1573 1080 : sc.push_back( "HB" );
1574 1080 : sc.push_back( "HG11" );
1575 1080 : sc.push_back( "HG12" );
1576 1080 : sc.push_back( "HG21" );
1577 1080 : sc.push_back( "HG22" );
1578 1080 : sc.push_back( "HG23" );
1579 1080 : sc.push_back( "1HG1" );
1580 1080 : sc.push_back( "2HG1" );
1581 1080 : sc.push_back( "1HG2" );
1582 1080 : sc.push_back( "2HG2" );
1583 1080 : sc.push_back( "3HG2" );
1584 1080 : sc.push_back( "HD1" );
1585 1080 : sc.push_back( "HD2" );
1586 1080 : sc.push_back( "HD3" );
1587 540 : return sc;
1588 5346 : } else if(s=="LEU") {
1589 1296 : sc.push_back( "CB" );
1590 1296 : sc.push_back( "CG" );
1591 1296 : sc.push_back( "CD1" );
1592 1296 : sc.push_back( "CD2" );
1593 1296 : sc.push_back( "HB1" );
1594 1296 : sc.push_back( "HB2" );
1595 1296 : sc.push_back( "HB3" );
1596 1296 : sc.push_back( "HG" );
1597 1296 : sc.push_back( "HD11" );
1598 1296 : sc.push_back( "HD12" );
1599 1296 : sc.push_back( "HD13" );
1600 1296 : sc.push_back( "HD21" );
1601 1296 : sc.push_back( "HD22" );
1602 1296 : sc.push_back( "HD23" );
1603 1296 : sc.push_back( "1HD1" );
1604 1296 : sc.push_back( "2HD1" );
1605 1296 : sc.push_back( "3HD1" );
1606 1296 : sc.push_back( "1HD2" );
1607 1296 : sc.push_back( "2HD2" );
1608 1296 : sc.push_back( "3HD2" );
1609 648 : return sc;
1610 4698 : } else if(s=="LYS") {
1611 2016 : sc.push_back( "CB" );
1612 2016 : sc.push_back( "CG" );
1613 2016 : sc.push_back( "CD" );
1614 2016 : sc.push_back( "CE" );
1615 2016 : sc.push_back( "NZ" );
1616 2016 : sc.push_back( "HB1" );
1617 2016 : sc.push_back( "HB2" );
1618 2016 : sc.push_back( "HB3" );
1619 2016 : sc.push_back( "HG1" );
1620 2016 : sc.push_back( "HG2" );
1621 2016 : sc.push_back( "HG3" );
1622 2016 : sc.push_back( "HD1" );
1623 2016 : sc.push_back( "HD2" );
1624 2016 : sc.push_back( "HD3" );
1625 2016 : sc.push_back( "HE1" );
1626 2016 : sc.push_back( "HE2" );
1627 2016 : sc.push_back( "HE3" );
1628 2016 : sc.push_back( "HZ1" );
1629 2016 : sc.push_back( "HZ2" );
1630 2016 : sc.push_back( "HZ3" );
1631 1008 : return sc;
1632 3690 : } else if(s=="MET") {
1633 576 : sc.push_back( "CB" );
1634 576 : sc.push_back( "CG" );
1635 576 : sc.push_back( "SD" );
1636 576 : sc.push_back( "CE" );
1637 576 : sc.push_back( "HB1" );
1638 576 : sc.push_back( "HB2" );
1639 576 : sc.push_back( "HB3" );
1640 576 : sc.push_back( "HG1" );
1641 576 : sc.push_back( "HG2" );
1642 576 : sc.push_back( "HG3" );
1643 576 : sc.push_back( "HE1" );
1644 576 : sc.push_back( "HE2" );
1645 576 : sc.push_back( "HE3" );
1646 288 : return sc;
1647 3402 : } else if(s=="PHE") {
1648 2196 : sc.push_back( "CB" );
1649 2196 : sc.push_back( "CG" );
1650 2196 : sc.push_back( "CD1" );
1651 2196 : sc.push_back( "CD2" );
1652 2196 : sc.push_back( "CE1" );
1653 2196 : sc.push_back( "CE2" );
1654 2196 : sc.push_back( "CZ" );
1655 2196 : sc.push_back( "HB1" );
1656 2196 : sc.push_back( "HB2" );
1657 2196 : sc.push_back( "HB3" );
1658 2196 : sc.push_back( "HD1" );
1659 2196 : sc.push_back( "HD2" );
1660 2196 : sc.push_back( "HD3" );
1661 2196 : sc.push_back( "HE1" );
1662 2196 : sc.push_back( "HE2" );
1663 2196 : sc.push_back( "HE3" );
1664 2196 : sc.push_back( "HZ" );
1665 1098 : return sc;
1666 2304 : } else if(s=="PRO") {
1667 216 : sc.push_back( "CB" );
1668 216 : sc.push_back( "CG" );
1669 216 : sc.push_back( "CD" );
1670 216 : sc.push_back( "HB1" );
1671 216 : sc.push_back( "HB2" );
1672 216 : sc.push_back( "HB3" );
1673 216 : sc.push_back( "HG1" );
1674 216 : sc.push_back( "HG2" );
1675 216 : sc.push_back( "HG3" );
1676 216 : sc.push_back( "HD1" );
1677 216 : sc.push_back( "HD2" );
1678 216 : sc.push_back( "HD3" );
1679 108 : return sc;
1680 2196 : } else if(s=="SER") {
1681 1260 : sc.push_back( "CB" );
1682 1260 : sc.push_back( "OG" );
1683 1260 : sc.push_back( "HB1" );
1684 1260 : sc.push_back( "HB2" );
1685 1260 : sc.push_back( "HB3" );
1686 1260 : sc.push_back( "HG1" );
1687 1260 : sc.push_back( "HG" );
1688 630 : return sc;
1689 1566 : } else if(s=="THR") {
1690 1548 : sc.push_back( "CB" );
1691 1548 : sc.push_back( "OG1" );
1692 1548 : sc.push_back( "CG2" );
1693 1548 : sc.push_back( "HB" );
1694 1548 : sc.push_back( "HG1" );
1695 1548 : sc.push_back( "HG21" );
1696 1548 : sc.push_back( "HG22" );
1697 1548 : sc.push_back( "HG23" );
1698 1548 : sc.push_back( "1HG2" );
1699 1548 : sc.push_back( "2HG2" );
1700 1548 : sc.push_back( "3HG2" );
1701 774 : return sc;
1702 792 : } else if(s=="TRP") {
1703 144 : sc.push_back( "CB" );
1704 144 : sc.push_back( "CG" );
1705 144 : sc.push_back( "CD1" );
1706 144 : sc.push_back( "CD2" );
1707 144 : sc.push_back( "NE1" );
1708 144 : sc.push_back( "CE2" );
1709 144 : sc.push_back( "CE3" );
1710 144 : sc.push_back( "CZ2" );
1711 144 : sc.push_back( "CZ3" );
1712 144 : sc.push_back( "CH2" );
1713 144 : sc.push_back( "HB1" );
1714 144 : sc.push_back( "HB2" );
1715 144 : sc.push_back( "HB3" );
1716 144 : sc.push_back( "HD1" );
1717 144 : sc.push_back( "HE1" );
1718 144 : sc.push_back( "HE3" );
1719 144 : sc.push_back( "HZ2" );
1720 144 : sc.push_back( "HZ3" );
1721 144 : sc.push_back( "HH2" );
1722 72 : return sc;
1723 720 : } else if(s=="TYR") {
1724 288 : sc.push_back( "CB" );
1725 288 : sc.push_back( "CG" );
1726 288 : sc.push_back( "CD1" );
1727 288 : sc.push_back( "CD2" );
1728 288 : sc.push_back( "CE1" );
1729 288 : sc.push_back( "CE2" );
1730 288 : sc.push_back( "CZ" );
1731 288 : sc.push_back( "OH" );
1732 288 : sc.push_back( "HB1" );
1733 288 : sc.push_back( "HB2" );
1734 288 : sc.push_back( "HB3" );
1735 288 : sc.push_back( "HD1" );
1736 288 : sc.push_back( "HD2" );
1737 288 : sc.push_back( "HD3" );
1738 288 : sc.push_back( "HE1" );
1739 288 : sc.push_back( "HE2" );
1740 288 : sc.push_back( "HE3" );
1741 288 : sc.push_back( "HH" );
1742 144 : return sc;
1743 576 : } else if(s=="VAL") {
1744 1152 : sc.push_back( "CB" );
1745 1152 : sc.push_back( "CG1" );
1746 1152 : sc.push_back( "CG2" );
1747 1152 : sc.push_back( "HB" );
1748 1152 : sc.push_back( "HG11" );
1749 1152 : sc.push_back( "HG12" );
1750 1152 : sc.push_back( "HG13" );
1751 1152 : sc.push_back( "HG21" );
1752 1152 : sc.push_back( "HG22" );
1753 1152 : sc.push_back( "HG23" );
1754 1152 : sc.push_back( "1HG1" );
1755 1152 : sc.push_back( "2HG1" );
1756 1152 : sc.push_back( "3HG1" );
1757 1152 : sc.push_back( "1HG2" );
1758 1152 : sc.push_back( "2HG2" );
1759 1152 : sc.push_back( "3HG2" );
1760 576 : return sc;
1761 0 : } else plumed_merror("Sidechain atoms unknown: " + s);
1762 : }
1763 :
1764 47016 : bool CS2Backbone::isSP2(const string & resType, const string & atomName) {
1765 : bool sp2 = false;
1766 47016 : if (atomName == "C") return true;
1767 43848 : if (atomName == "O") return true;
1768 :
1769 40716 : if(resType == "TRP") {
1770 396 : if (atomName == "CG") sp2 = true;
1771 378 : else if (atomName == "CD1") sp2 = true;
1772 360 : else if (atomName == "CD2") sp2 = true;
1773 342 : else if (atomName == "CE2") sp2 = true;
1774 324 : else if (atomName == "CE3") sp2 = true;
1775 306 : else if (atomName == "CZ2") sp2 = true;
1776 288 : else if (atomName == "CZ3") sp2 = true;
1777 270 : else if (atomName == "CH2") sp2 = true;
1778 40320 : } else if (resType == "ASP") {
1779 1656 : if (atomName == "CG") sp2 = true;
1780 1494 : else if (atomName == "OD1") sp2 = true;
1781 1332 : else if (atomName == "OD2") sp2 = true;
1782 38664 : } else if (resType == "GLU") {
1783 2844 : if (atomName == "CD") sp2 = true;
1784 2628 : else if (atomName == "OE1") sp2 = true;
1785 2412 : else if (atomName == "OE2") sp2 = true;
1786 35820 : } else if (resType == "ARG") {
1787 2772 : if (atomName == "CZ") sp2 = true;
1788 33048 : } else if (resType == "HIS") {
1789 0 : if (atomName == "CG") sp2 = true;
1790 0 : else if (atomName == "ND1") sp2 = true;
1791 0 : else if (atomName == "CD2") sp2 = true;
1792 0 : else if (atomName == "CE1") sp2 = true;
1793 0 : else if (atomName == "NE2") sp2 = true;
1794 33048 : } else if (resType == "PHE") {
1795 5184 : if (atomName == "CG") sp2 = true;
1796 4896 : else if (atomName == "CD1") sp2 = true;
1797 4608 : else if (atomName == "CD2") sp2 = true;
1798 4320 : else if (atomName == "CE1") sp2 = true;
1799 4032 : else if (atomName == "CE2") sp2 = true;
1800 3744 : else if (atomName == "CZ") sp2 = true;
1801 27864 : } else if (resType == "TYR") {
1802 684 : if (atomName == "CG") sp2 = true;
1803 648 : else if (atomName == "CD1") sp2 = true;
1804 612 : else if (atomName == "CD2") sp2 = true;
1805 576 : else if (atomName == "CE1") sp2 = true;
1806 540 : else if (atomName == "CE2") sp2 = true;
1807 504 : else if (atomName == "CZ") sp2 = true;
1808 27180 : } else if (resType == "ASN") {
1809 1944 : if (atomName == "CG") sp2 = true;
1810 1782 : else if (atomName == "OD1") sp2 = true;
1811 25236 : } else if (resType == "GLN") {
1812 810 : if (atomName == "CD") sp2 = true;
1813 756 : else if (atomName == "OE1") sp2 = true;
1814 : }
1815 :
1816 40716 : return sp2;
1817 : }
1818 :
1819 145728 : bool CS2Backbone::is_chi1_cx(const string & frg, const string & atm) {
1820 145728 : if(atm=="CG") return true;
1821 139788 : if((frg == "CYS")&&(atm =="SG")) return true;
1822 288792 : if(((frg == "ILE")||(frg == "VAL"))&&(atm == "CG1")) return true;
1823 145602 : if((frg == "SER")&&(atm == "OG")) return true;
1824 148878 : if((frg == "THR")&&(atm == "OG1")) return true;
1825 :
1826 137268 : return false;
1827 : }
1828 :
1829 3599784 : void CS2Backbone::xdist_name_map(string & name) {
1830 7199568 : if((name == "OT1")||(name == "OC1")) name = "O";
1831 10799352 : else if ((name == "HN") || (name == "HT1") || (name == "H1")) name = "H";
1832 10737144 : else if ((name == "CG1")|| (name == "OG")||
1833 7159572 : (name == "SG") || (name == "OG1")) name = "CG";
1834 7040070 : else if ((name == "HA1")|| (name == "HA3")) name = "HA";
1835 3599784 : }
1836 :
1837 18 : void CS2Backbone::update() {
1838 : // write status file
1839 36 : if(getWstride()>0&& (getStep()%getWstride()==0 || getCPT()) ) writeStatus();
1840 18 : }
1841 :
1842 : }
1843 5874 : }
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